I have no such problems with 2.5
or
the beta, unless i mess things up outside of lightroom, but i have no reason to even go outside of lightroom. There is the 'Synchronize folder' button if you do need to fix things.. But if you have to you're simply doing it wrong..

If i use PNG it will be with export, and things i export i do not want to show in my library. Why would anyone. All the managing options are there, maybe you need to be more creative with it.